RNA structure analysis : algorithms and applications
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[1] P. Green,et al. Ancient conserved regions in new gene sequences and the protein databases. , 1993, Science.
[2] Graziano Pesole,et al. PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences , 2003, Nucleic Acids Res..
[3] Dan Gusfield. Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .
[4] C. Sander,et al. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III , 1992, Protein science : a publication of the Protein Society.
[5] I. Hofacker,et al. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. , 2004, Journal of molecular biology.
[6] Michael J. Fischer,et al. The String-to-String Correction Problem , 1974, JACM.
[7] S. Eddy,et al. A computational screen for methylation guide snoRNAs in yeast. , 1999, Science.
[8] Bin Tian,et al. A large-scale analysis of mRNA polyadenylation of human and mouse genes , 2005, Nucleic acids research.
[9] Bjarne Knudsen,et al. Pfold: RNA Secondary Structure Prediction Using Stochastic Context-Free Grammars , 2003 .
[10] James R. Cole,et al. Alignment of possible secondary structures in multiple RNA sequences using simulated annealing , 1996, Comput. Appl. Biosci..
[11] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[12] Jun Hu,et al. A method for aligning RNA secondary structures and its application to RNA motif detection , 2005, BMC Bioinformatics.
[13] Thomas Dandekar,et al. A software tool-box for analysis of regulatory RNA elements , 2003, Nucleic Acids Res..
[14] C. Y. Chen,et al. AU-rich elements: characterization and importance in mRNA degradation. , 1995, Trends in biochemical sciences.
[15] D. Haussler,et al. Using multiple alignments and phylogenetic trees to detect RNA secondary structure. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[16] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[17] S. Karlin,et al. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[18] Graziano Pesole,et al. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance , 2000, Bioinform..
[19] S. Le,et al. Prediction of common secondary structures of RNAs: a genetic algorithm approach. , 2000, Nucleic acids research.
[20] R. Durbin,et al. RNA sequence analysis using covariance models. , 1994, Nucleic acids research.
[21] D. Higgins,et al. RAGA: RNA sequence alignment by genetic algorithm. , 1997, Nucleic acids research.
[22] G. Mauri,et al. An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences , 2008, Journal of Computer Science and Technology.
[23] S. Kuersten,et al. The power of the 3′ UTR: translational control and development , 2003, Nature Reviews Genetics.
[24] D. Ecker,et al. RNAMotif, an RNA secondary structure definition and search algorithm. , 2001, Nucleic acids research.
[25] Kaizhong Zhang,et al. Comparing multiple RNA secondary structures using tree comparisons , 1990, Comput. Appl. Biosci..
[26] R. C. Underwood,et al. Stochastic context-free grammars for tRNA modeling. , 1994, Nucleic acids research.
[27] Hélène Touzet,et al. Finding the common structure shared by two homologous RNAs , 2003, Bioinform..
[28] N. Gray,et al. Regulation of mRNA translation by 5'- and 3'-UTR-binding factors. , 2003, Trends in biochemical sciences.
[29] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[30] D. Turner,et al. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. , 2002, Journal of molecular biology.
[31] G. Stormo,et al. A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. , 2004, Bioinformatics.
[32] Sean R. Eddy,et al. Rfam: an RNA family database , 2003, Nucleic Acids Res..
[33] Gary D. Stormo,et al. Phylogenetically enhanced statistical tools for RNA structure prediction , 2000, Bioinform..
[34] Tala Bakheet,et al. ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins , 2001, Nucleic Acids Res..
[35] Daniel Gautheret,et al. An RNA pattern matching program with enhanced performance and portability , 1994, Comput. Appl. Biosci..
[36] D. Gautheret,et al. Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. , 2001, Journal of molecular biology.
[37] Robert Giegerich,et al. Local similarity in RNA secondary structures , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.
[38] Jon D. McAuliffe,et al. Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome , 2003, Science.
[39] R. Duronio,et al. Histone mRNA expression: multiple levels of cell cycle regulation and important developmental consequences. , 2002, Current opinion in cell biology.
[40] Eugene W. Myers,et al. Optimal alignments in linear space , 1988, Comput. Appl. Biosci..
[41] P. Stadler,et al. Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.
[42] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[43] J. Sabina,et al. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.
[44] K. Katz,et al. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. , 2000, Trends in genetics : TIG.
[45] K. Lindblad-Toh,et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.
[46] D. Landsman,et al. Statistical analysis of over-represented words in human promoter sequences. , 2004, Nucleic acids research.
[47] Ivo L. Hofacker,et al. Vienna RNA secondary structure server , 2003, Nucleic Acids Res..
[48] E Rivas,et al. A dynamic programming algorithm for RNA structure prediction including pseudoknots. , 1998, Journal of molecular biology.
[49] M. Blanchette,et al. Discovery of regulatory elements by a computational method for phylogenetic footprinting. , 2002, Genome research.
[50] Michael Q. Zhang,et al. Identifying tissue-selective transcription factor binding sites in vertebrate promoters. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[51] Graziano Pesole,et al. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs , 2000, Nucleic Acids Res..
[52] Bin Ma,et al. A General Edit Distance between RNA Structures , 2002, J. Comput. Biol..
[53] Bruce A. Shapiro,et al. An algorithm for comparing multiple RNA secondary structures , 1988, Comput. Appl. Biosci..
[54] Laurie J. Heyer,et al. Finding the most significant common sequence and structure motifs in a set of RNA sequences. , 1997, Nucleic acids research.
[55] J. Wilusz,et al. Bringing the role of mRNA decay in the control of gene expression into focus. , 2004, Trends in genetics : TIG.
[56] Michael S. Waterman,et al. Linear Trees and RNA Secondary Structure , 1994, Discret. Appl. Math..
[57] Ian Holmes,et al. Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars , 2001, Pacific Symposium on Biocomputing.
[58] Sean R. Eddy,et al. RSEARCH: Finding homologs of single structured RNA sequences , 2003, BMC Bioinformatics.
[59] G. Stormo,et al. Discovering common stem-loop motifs in unaligned RNA sequences. , 2001, Nucleic acids research.
[60] D. Turner,et al. Improved predictions of secondary structures for RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[61] Daniel S. Hirschberg,et al. A linear space algorithm for computing maximal common subsequences , 1975, Commun. ACM.
[62] S. Eddy,et al. Computational identification of noncoding RNAs in E. coli by comparative genomics , 2001, Current Biology.
[63] G. Ruvkun,et al. A uniform system for microRNA annotation. , 2003, RNA.
[64] D. Bartel. MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.
[65] D. Sankoff. Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems , 1985 .
[66] M. Zuker. On finding all suboptimal foldings of an RNA molecule. , 1989, Science.
[67] Gary D. Stormo,et al. A Phylogenetic Approach to RNA Structure Prediction , 1999, ISMB.
[68] Bin Ma,et al. Edit distance between two RNA structures , 2001, RECOMB.
[69] Kaizhong Zhang,et al. A new algorithm for computing similarity between RNA structures , 2001, Inf. Sci..
[70] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.